Animal Molecular Breeding 2024, Vol.14, No.1, 119-129 http://animalscipublisher.com/index.php/amb 124 4.2 Case study on genetic diversity Marker-Assisted Selection (MAS) has been instrumental in enhancing genetic diversity within sheep breeding programs (Figure 3). A notable study investigated the genetic diversity and selection signals in 14 indigenous sheep breeds from the Middle East and South Asia, including breeds from Iran, Afghanistan, India, and Bangladesh (Eydivandi et al., 2021). The study utilized SNP genotype data to detect genetic diversity and population structure through various analyses such as principal component analysis (PCA), admixture, phylogenetic analyses, and Runs of Homozygosity. The results revealed significant genetic diversity among the breeds, with several genomic regions identified as candidates for selective sweeps. These regions were associated with economically important traits such as disease resistance and climate adaptation, highlighting the potential of MAS to enhance genetic diversity and improve breed resilience (Eydivandi et al., 2021). Li et al. (2020) provided offers a comprehensive genetic analysis of sheep horn number variation, combining genome-wide association studies and selective sweep analyses to identify key genetic markers. By analyzing phenotypes across different sheep breeds, the study highlights the significance of specific genes, such as HOXD1 on chromosome 2 and RXFP2 on chromosome 10, which are associated with horn development and polled (hornless) traits. The findings are visualized through detailed Manhattan plots, which clearly illustrate significant genetic loci. Furthermore, the study expands beyond horn traits to explore genetic associations with other economically important traits like reproduction and milk yield, utilizing a large dataset of CNVs and SNPs. This integrated approach not only pinpoints genetic variants influencing phenotypic diversity but also offers potential targets for breeding programs focused on specific traits, demonstrating the power of genetic technologies in agricultural improvements. 4.3 Comparative case studies Marker-Assisted Selection (MAS) has been applied in various pig breeding programs across different regions, yielding diverse outcomes. For instance, in a study conducted in the United States, MAS was employed to enhance growth rate and meat quality in pigs. The results demonstrated significant improvements in these traits, leading to increased productivity and profitability for pig farmers (Singh et al., 2022). Conversely, a similar study in Europe focused on disease resistance, particularly against Porcine Reproductive and Respiratory Syndrome (PRRS). The application of MAS in this context resulted in a notable reduction in disease incidence, although the overall impact on growth performance was less pronounced compared to the U.S. study (Moriguchi et al., 2020). In Asia, MAS has been utilized to improve reproductive traits in pigs, such as litter size and weaning weight. The outcomes of these programs have been mixed, with some studies reporting substantial gains in reproductive efficiency, while others have observed only marginal improvements (Vion et al., 2021). These contrasting results highlight the importance of considering regional differences in genetic backgrounds, environmental conditions, and breeding objectives when implementing MAS in pig breeding programs. 4.4 Innovative applications of MAS Recent advancements in genomic technologies have enabled the integration of innovative approaches with MAS in dairy and beef cattle breeding. One notable example is the use of genomic selection (GS) to enhance milk production and quality in dairy cattle. A study conducted in the United States demonstrated that combining MAS with GS significantly increased the accuracy of selecting high-yielding dairy cows, leading to substantial improvements in milk yield and composition (Kushanov et al., 2021). Similarly, in beef cattle, the integration of MAS with GS has been employed to improve traits such as feed efficiency and meat quality. In a study conducted in Australia, this combined approach resulted in significant gains in feed conversion ratios and marbling scores, thereby enhancing the overall profitability of beef production (Darmanov et al., 2022). Another innovative application of MAS in cattle breeding involves the use of high-resolution melting (HRM)-based markers to accelerate the development of disease-resistant breeds. For instance, a study in Brazil utilized HRM markers to identify and select cattle with resistance to bovine respiratory disease, leading to a notable reduction in disease prevalence and associated economic losses (Wang et al., 2023). These case studies illustrate the potential of integrating new technologies with MAS to achieve more precise and efficient breeding outcomes in dairy and beef cattle.
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